I can not install packages named 'ChIPpeakAnno' or 'ChIPseeker' from BiocManager. It always says that a package named 'GenomeInfoDb' can't be loaded.
And when I tried to install 'GenomeInfoDb', it says: installation of package ‘GenomeInfoDbData’ had non-zero exit status.
I've reinstalled R and R studio, and tried to run R studio as administrator, it didn't work.
> library(ChIPseeker)
Error: package or namespace load failed for ‘ChIPseeker’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
‘GenomeInfoDbData’ という名前のパッケージはありません
> BiocManager::install('GenomeInfoDbData')
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details
replacement repositories:
CRAN: https://cran.rstudio.com/
Bioconductor version 3.15 (BiocManager 1.30.18), R 4.2.1 (2022-06-23 ucrt)
Installing package(s) 'GenomeInfoDbData'
ソースパッケージ ‘GenomeInfoDbData’ をインストール中です
trying URL 'https://bioconductor.org/packages/3.15/data/annotation/src/contrib/GenomeInfoDbData_1.2.8.tar.gz'
Content type 'application/x-gzip' length 11512907 bytes (11.0 MB)
downloaded 11.0 MB
Error in file(filename, "r", encoding = encoding) :
cannot open the connection
Calls: source -> file
In addition: Warning message:
In file(filename, "r", encoding = encoding) :
cannot open file 'renv/activate.R': No such file or directory
Execution halted
ダウンロードされたパッケージは、以下にあります
‘C:\Users\ilove\AppData\Local\Temp\RtmpcFS51Z\downloaded_packages’
Old packages: 'Matrix', 'openssl'
Update all/some/none? [a/s/n]:
a
利用できるバイナリー版がありますがソース版は後者です:
binary source needs_compilation
Matrix 1.5-0 1.5-1 TRUE
openssl 2.0.2 2.0.3 TRUE
Binaries will be installed
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.2/Matrix_1.5-0.zip'
Content type 'application/zip' length 4512813 bytes (4.3 MB)
downloaded 4.3 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.2/openssl_2.0.2.zip'
Content type 'application/zip' length 2645671 bytes (2.5 MB)
downloaded 2.5 MB
パッケージ ‘Matrix’ は無事に展開され、MD5 サムもチェックされました
パッケージ ‘openssl’ は無事に展開され、MD5 サムもチェックされました
ダウンロードされたパッケージは、以下にあります
C:\Users\ilove\AppData\Local\Temp\RtmpcFS51Z\downloaded_packages
Warning message:
In install.packages(...) :
パッケージ ‘GenomeInfoDbData’ のインストールは、ゼロでない終了値をもちました
> BiocManager::install('GenomeInfoDbData')
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details
replacement repositories:
CRAN: https://cran.rstudio.com/
Bioconductor version 3.15 (BiocManager 1.30.18), R 4.2.1 (2022-06-23 ucrt)
Installing package(s) 'GenomeInfoDbData'
ソースパッケージ ‘GenomeInfoDbData’ をインストール中です
trying URL 'https://bioconductor.org/packages/3.15/data/annotation/src/contrib/GenomeInfoDbData_1.2.8.tar.gz'
Content type 'application/x-gzip' length 11512907 bytes (11.0 MB)
downloaded 11.0 MB
Error in file(filename, "r", encoding = encoding) :
cannot open the connection
Calls: source -> file
In addition: Warning message:
In file(filename, "r", encoding = encoding) :
cannot open file 'renv/activate.R': No such file or directory
Execution halted
ダウンロードされたパッケージは、以下にあります
‘C:\Users\ilove\AppData\Local\Temp\RtmpcFS51Z\downloaded_packages’
Old packages: 'Matrix', 'openssl'
Update all/some/none? [a/s/n]:
n
Warning message:
In install.packages(...) :
パッケージ ‘GenomeInfoDbData’ のインストールは、ゼロでない終了値をもちました
> sessionInfo()
R version 4.2.1 (2022-06-23 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 22000)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.932 LC_CTYPE=English_United States.932 LC_MONETARY=English_United States.932
[4] LC_NUMERIC=C LC_TIME=English_United States.932
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] IRanges_2.30.1 digest_0.6.29 bitops_1.0-7 stats4_4.2.1 evaluate_0.16 rlang_1.0.5 cli_3.4.0
[8] S4Vectors_0.34.0 rmarkdown_2.16 tools_4.2.1 RCurl_1.98-1.8 xfun_0.33 yaml_2.3.5 fastmap_1.1.0
[15] compiler_4.2.1 BiocGenerics_0.42.0 BiocManager_1.30.18 htmltools_0.5.3 knitr_1.40
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